Genetic susceptibility to malaria and other infectious diseases: from the MHC to the whole genome

Parasitology ◽  
1996 ◽  
Vol 112 (S1) ◽  
pp. S75-S84 ◽  
Author(s):  
A. V. S. Hill
Keyword(s):  
Infectious Diseases ◽  
Twin Studies ◽  
Susceptibility Genes ◽  
Human Populations ◽  
Whole Genome ◽  
Case Control Studies ◽  
Powerful Approach ◽  
Affected Sibling Pair ◽  
Important Host ◽  
Host Genetic

There is substantial evidence that host genetic factors play a major role in determining the outcome of infection with many pathogens. Detailed analysis of malaria has identified twelve genes that affect susceptibility in various human populations. However, less attention has been paid to other major infectious diseases where twin studies have identified an important host genetic component to susceptibility. Recent progress in the analysis of the human genome offers exciting prospects for the mapping and identification of new susceptibility and resistance genes for common infectious diseases. Screening of the whole genome in affected sibling pair studies is now feasible by employing highly informative microsatellite markers. In addition, many polymorphic candidate genes have become available for analysis in case-control studies. It is proposed that these new genetic tools offer a powerful approach to the epidemiological analysis of many infectious diseases in humans and supersede traditional genetic approaches to identifying susceptibility genes in mouse models. Progress in characterizing the role of major histocompatibility genes in susceptibility to malaria and other infectious diseases is reviewed before outlining the methodologies for and progress in identifying non-MHC susceptibility genes.

scholarly journals A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome

2021 ◽  
Author(s):  
Seyoung Mun ◽  
Songmi Kim ◽  
Wooseok Lee ◽  
Keunsoo Kang ◽  
Thomas J. Meyer ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Personal Genome ◽  
Human Populations ◽  
Whole Genome ◽  
Structural Variations ◽  
Insert Size ◽  
Human Genomes ◽  
Next Generation Sequencing Ngs

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

scholarly journals An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

2020 ◽  
Author(s):  
John-Sebastian Eden ◽  
Rebecca Rockett ◽  
Ian Carter ◽  
Hossinur Rahman ◽  
Joep de Ligt ◽  
...  
Keyword(s):  
New Zealand ◽  
Infectious Diseases ◽  
Genome Sequencing ◽  
Phylogenetic Analyses ◽  
Emerging Infectious Diseases ◽  
Whole Genome Sequencing Data ◽  
Viral Diversity ◽  
Whole Genome ◽  
Sequencing Data ◽  
Public Data

AbstractThe SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea and Iran. Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.

scholarly journals Patterns of smallpox mortality in London, England, over three centuries

PLoS Biology ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. e3000506
Author(s):  
Olga Krylova ◽  
David J. D. Earn
Keyword(s):  
Public Health ◽  
Infectious Disease ◽  
Time Series ◽  
Spectral Analysis ◽  
Infectious Diseases ◽  
Health Policies ◽  
Human Populations ◽  
Public Health Policies ◽  
History Of ◽  
History Of Control

Smallpox is unique among infectious diseases in the degree to which it devastated human populations, its long history of control interventions, and the fact that it has been successfully eradicated. Mortality from smallpox in London, England was carefully documented, weekly, for nearly 300 years, providing a rare and valuable source for the study of ecology and evolution of infectious disease. We describe and analyze smallpox mortality in London from 1664 to 1930. We digitized the weekly records published in the London Bills of Mortality (LBoM) and the Registrar General’s Weekly Returns (RGWRs). We annotated the resulting time series with a sequence of historical events that might have influenced smallpox dynamics in London. We present a spectral analysis that reveals how periodicities in reported smallpox mortality changed over decades and centuries; many of these changes in epidemic patterns are correlated with changes in control interventions and public health policies. We also examine how the seasonality of reported smallpox mortality changed from the 17th to 20th centuries in London.

scholarly journals Draft Genome Sequence of Streptococcus suis S10, a Virulent Strain Used in Experimental Pig Infections

2019 ◽  
Vol 8 (23) ◽  
Author(s):  
Rogier A. Gaiser ◽  
Aldert L. Zomer ◽  
Jerry M. Wells ◽  
Peter van Baarlen
Keyword(s):  
Infectious Diseases ◽  
Genome Sequence ◽  
Virulent Strain ◽  
Draft Genome ◽  
Streptococcus Suis ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Highly Virulent

Here, we report the draft whole-genome sequence of Streptococcus suis strain S10, isolated from the tonsils of a healthy pig. S. suis S10 belongs to the highly virulent serotype 2, which includes isolates that cause infectious diseases, including meningitis, in pigs and human.

scholarly journals Insights on Population Structure and Within-Host Genetic Changes among Meningococcal Carriage Isolates from U.S. Universities

mSphere ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Sandeep J. Joseph ◽  
Nadav Topaz ◽  
How-Yi Chang ◽  
Melissa J. Whaley ◽  
Jeni T. Vuong ◽  
...  
Keyword(s):  
General Population ◽  
Neisseria Meningitidis ◽  
Meningococcal Disease ◽  
Mass Vaccination ◽  
Invasive Meningococcal Disease ◽  
Whole Genome ◽  
Genetic Changes ◽  
Content Type ◽  
Host Genetic ◽  
Vaccination Campaigns

ABSTRACT In 2015 and 2016, meningococcal carriage evaluations were conducted at two universities in the United States following mass vaccination campaigns in response to Neisseria meningitidis serogroup B (NmB) disease outbreaks. A simultaneous carriage evaluation was also conducted at a university near one of the outbreaks, where no NmB cases were reported and no mass vaccination occurred. A total of ten cross-sectional carriage evaluation rounds were conducted, resulting in 1,514 meningococcal carriage isolates collected from 7,001 unique participants; 1,587 individuals were swabbed at multiple time points (repeat participants). All isolates underwent whole-genome sequencing. The most frequently observed clonal complexes (CC) were CC198 (27.3%), followed by CC1157 (17.4%), CC41/44 (9.8%), CC35 (7.4%), and CC32 (5.6%). Phylogenetic analysis identified carriage isolates that were highly similar to the NmB outbreak strains; comparative genomics between these outbreak and carriage isolates revealed genetic changes in virulence genes. Among repeat participants, 348 individuals carried meningococcal bacteria during at least one carriage evaluation round; 50.3% retained N. meningitidis carriage of a strain with the same sequence type (ST) and CC across rounds, 44.3% only carried N. meningitidis in one round, and 5.4% acquired a new N. meningitidis strain between rounds. Recombination, point mutations, deletions, and simple sequence repeats were the most frequent genetic mechanisms found in isolates collected from hosts carrying a strain of the same ST and CC across rounds. Our findings provide insight on the dynamics of meningococcal carriage among a population that is at higher risk for invasive meningococcal disease than the general population. IMPORTANCE U.S. university students are at a higher risk of invasive meningococcal disease than the general population. The responsible pathogen, Neisseria meningitidis, can be carried asymptomatically in the oropharynx; the dynamics of meningococcal carriage and the genetic features that distinguish carriage versus disease states are not completely understood. Through our analyses, we aimed to provide data to address these topics. We whole-genome sequenced 1,514 meningococcal carriage isolates from individuals at three U.S. universities, two of which underwent mass vaccination campaigns following recent meningococcal outbreaks. We describe the within-host genetic changes among individuals carrying a strain with the same molecular type over time, the primary strains being carried in this population, and the genetic differences between closely related outbreak and carriage strains. Our results provide detailed information on the dynamics of meningococcal carriage and the genetic differences in carriage and outbreak strains, which can inform future efforts to reduce the incidence of invasive meningococcal disease.

scholarly journals Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Reuben J. Pengelly ◽  
William Tapper ◽  
Jane Gibson ◽  
Marcin Knut ◽  
Rick Tearle ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Human Populations ◽  
Whole Genome ◽  
Linkage Disequilibrium Structure ◽  
Genome Sequences
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